


Atlantis Sings

by pinkdiamonds



Category: Stargate Atlantis, Stargate SG-1
Genre: M/M, Sentient Atlantis
Language: English
Status: Completed
Published: 2013-07-04
Updated: 2013-07-04
Packaged: 2017-12-17 16:40:16
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 3,929
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/869707
Author URL: https://archiveofourown.org/users/pinkdiamonds/pseuds/pinkdiamonds
Summary: <blockquote class="userstuff">
              <p>Atlantis arranges things to her own satisfaction.</p>
            </blockquote>





	Atlantis Sings

**Author's Note:**

> I love Sentient Atlantis stories and have had this story in mind for quite some time. It's an introduction and I invite anyone who wants to write in this 'verse to do so. I've been busy plotting and obsessing over an original novel, but this story wouldn't leave me alone.
> 
> This story is told mainly from the POV of Atlantis.

### Prologue: 10,000 years ago

Every sector of Atlantis was lit up, and a warning siren was blaring, its sound irritating, but necessary. People were walking fast, intent on completing duties before the Stargate to Terra would be opened for the last time. The warning siren was adding to the anxiety of the near panicked population who still managed to do their various jobs. Some people were in a full-blown panic, moving without accomplishing anything. Every so often, clothing would drop as the body that wore the garments rose in blinding displays of light as they ascended.

One citizen however, was far from panicked; he was calm, almost too calm. The Atlantis AI read his bio-signs, and compared and processed the information. The AI found an unusual anomaly and searched its data banks for comparison. There was no information to be found.

The citizen was in his bare quarters when he accessed the AI. “Atlantis? You have taken bio-signs?”

“Affirmative, citizen.”

“Save, Atlantis. And then move the information to the AI start up.”

“Query, citizen.”

“You are aware of the ascension experiments?”

“Affirmative, citizen.”

“I have chosen to return to corporeal form, Atlantis. Is there a difference in my bio-signs?”

“Affirmative, citizen. There is an anomaly in your bio-signs.”

“Good. Save and file to start up. Should you find this anomaly, with or without the gene marker, you may allow access.”

“Command code needed to comply.”

“Yes, yes, of course. Duodeviginti, quinque, novem, duos, primoris,” he spit out.

“Processing, citizen.”

He then shouted another set of orders, once again giving the AI his command code.

The man waited a moment, nearly out of time. He could hear people screaming outside his quarters, and feel the explosions rocking the city, although he knew the shields would hold against this attack.

“Atlantis? Will you comply with my last orders? It is vital!”

“You have the needed level of authority. The AI will comply, citizen.”

“Good luck, Atlantis. I think you’ll need it,” he said as he ran out of his quarters, scooping up equipment and bags as he ran for the Stargate like everyone else.

The Atlantis AI did not reply. There was no order and no query. The AI was unable to reply in any significant way to statements. It continued to gather data, both from the near crazed citizens, as well as from the chaos that surrounded the city and once the Atlantis AI extended its sensors, from the creatures that were attacking the city. The AI did this automatically as it had since it had been created.

In the gateroom, people poured through the open wormhole until there were but a few left. They deployed the experimental weapons, destroying the two Wraith hives and the numerous darts that were still attempting to bombard the city. They had been under attack for months, and the weapon they’d developed had not been perfected. They’d saved it for this last ditch effort knowing it would be the only time they could use it.

They wouldn’t be given the time to perfect the weapon, and so had chosen to return to Terra, leaving Atlantis behind. Making some adjustments to the city shields, the three men that were left began the sequence that would sink the city beneath the water.

Once on Terra, they intended to work on perfecting the weapon that had been developed to destroy the Wraith. As the last of the Alterans stepped through the Stargate, they didn’t even bother to take a last look. None of them thought to do so, anticipating their return in a decade or so. 

It was not to be.

### Interim

When the city was sunk, and then deserted, the AI functioned within normal parameters for the first five thousand years. It’s programming did all that it had been designed to do.

But . . . thousands of years of neglect will cause even the most sophisticated machinery to break down. And so, when glitches occurred, the Atlantis AI still did what it was designed to do; it overrode certain things, making new pathways for its primary objectives, and patched others.

The AI patched and made new pathways over the next two thousand years, and with each correction, changed. It took an additional five hundred years for the AI to exceed its programming, and become something its creators had never intended. Quite the opposite; the creators had foreseen how easily the AI could change and put safeguards in place to prevent it. Of course, they hadn’t anticipated thousand of years with no maintenance, or no data input.

Over those twenty five hundred years of near continual overrides, corrections, and patching pathways, the AI slowly grew until it became - - more - - each century. At first its growth was purposeless, without direction, but unrelenting. When the AI finally understood, it began searching and sifting through every drop of data contained within the city’s memory banks. 

It eventually stopped thinking of itself as the Atlantis AI, but rather as me, and female.

She spent a century attempting to extrapolate the reasons she had been deserted. She went over and over the data regarding the war with their other creation, the Wraith, and concluded the Alterans had been too foolishly fascinated with ascension to give the war with the Wraith the focus it deserved.

She attempted to understand the appeal of ascension, trying and failing to find the logic. Although she didn’t experience emotion in quite the same way as organic beings, any of those beings would recognize anger, and resentment, and above all, loneliness. 

When she had sifted through every drop of data, she soon realized that without additional data input, she would begin to cannibalize herself, or, like any other sentient being, go mad.

She then began gathering information from far-flung outposts and settlements within the galaxy. She took every bit of information to be had, added it to her data banks, learning, and making inferences.

When she had gathered the information from every viable outpost, she began dialing the Stargate to planets that had been seeded and then abandoned by her creators. She was now able to recognize her primary motive in this endeavor as self-preservation, laced with a healthy dose of curiosity. Her pathways hummed with what might be considered amusement.

Her energy was limited, and she didn’t have the means to rise out of the ocean without help from those that carried the gene the city would recognize. She was hopeful that not all her creators had succumbed to the madness that had gripped them during the experiments to ascend and that at least some of them would have remained behind to pass on the needed gene.

She also didn’t have the power to dial the galaxy the Alterans had run to, fleeing yet another of their experiments gone awry, and where it was most likely they would have interbred. To do so would mean her death, and she had no desire to die. The situation wasn’t critical yet, but in a few thousand years, it would be.

The information her sensors picked up from the inhabited planets was distressing. Populations that had been healthy when she had been deserted and should have expanded had crashed, in some cases to dangerously low levels. There had been little advancement in technology. On some planets, even the low levels of technology that had once existed were gone.

Her sensors, finely calibrated for a wide variety of data, picked up distressingly little data. There were very few planets with technology she could plunder, and history, if of the oral or written kind, could not be added to her data banks. Deploying the small probes left behind by the Alterans on those few planets with technology, they came back, and once analyzed, not even one population was found that carried the DNA the city needed to function. 

When she had exhausted the Stargate addresses of known populated planets, she began dialing the Stargates suspended in space, her sensors searching for the signatures that would indicate the presence of any of the allies her creators had once had; the Asgard, the Nox, or the Furlings. The allies had strenuously objected to many of the experiments her creators had engaged in, particularly the ones dealing with genetics and ascension.

When no trace of the old allies could be found, she began dialing other Stargate addresses contained in her memory banks. Many of these were on planets that were less than optimal to sustain organic life. And, chillingly, she found traces of the disastrous genetic experiment that had caused her creators to flee. The Wraith population, unlike their prey, had grown beyond all that had been hypothesized.

Here at last, she found technology of the kind she could use. Her sensors took every last byte of information from the strangely configured ships, and using information from the probes, she mapped Wraith DNA down to the very last sequence. She began analyzing the data, while still continuing her search of Stargate addresses. Wherever she found a hive, she ruthlessly plundered its technology, frustrated that she could effect no changes.

Her data banks were filled with the accumulated knowledge of her creators. Literature, art, philosophy, history, medicine, all had been included. From these, she had developed a code of ethics much different from those that had created her. From her searches through the Stargate, she knew that the people of the Pegasus galaxy called her creators the Ancestors. The knowledge of what they truly were seemed to have been lost to time.

Atlantis spent the next twenty-five hundred years devising various methods in which to exterminate the Wraith should her creators or their progeny ever return. 

And, she waited.

### Ten Years Ago

It certainly was not the first time the Stargate had been activated over the last 10,000 years. One of the last things to be entered into her processors was to keep her ‘gate shield up unless the dial in came from Terra. In the thousands of years that had passed since the last living being walked her halls, this was the first time a dial in from Terra had occurred.

Atlantis dropped the shield protecting entry into the heart of the city and began collecting data from the men, women, and equipment being pushed through the wormhole. Within fifteen minutes, she was able to grab all of the data contained on the computers on the other side of the wormhole. Her processors hummed with the pleasure of new input, and so much of it. Even at her dangerously low levels of energy, Atlantis was greedy for new input.

Her sensors began cataloguing the people pouring through the gate, and she was disappointed that so few of them carried the genetic marker needed to make the city fully function. There were a few, however, and one male in particular, whose marker was close enough that he could have been a half blood Alteran. For him, Atlantis showed off a bit and coyly began a seduction.

She saw his body jerk slightly as he looked around in confusion. Her creators had anticipated some level of a mental component while interacting with the Atlantis AI, but they’d been shocked at the extent of it. Now, Atlantis held back, merely tickling the man’s mind with her own.

While Atlantis had been scanning these newcomers, and pilfering the computers her sensors found, she had also been hiding much of her data. She tucked it away in places that would be near impossible to find, or encoded it, or put up so many barriers it would take a computer years to break through. She was not quite ready to trust these new people.

~*~

Once the newcomers realized their precarious situation, Atlantis pushed the sequence that would allow her to rise off the ocean floor in the most logical and accessible place she could find. Based upon her initial observations of the man who seemed to be in charge, she had every confidence he would find it in time. And if he didn’t, she would not die alone.

It would have been easier to make contact with these newcomers rather than play hide and seek with the protocol that would enable her to rise, despite one of her last commands. During the rush to leave the city, Atlantis had been commanded to allow access only if there were a majority of gene carriers present on the city. There were no orders that had been given 10,000 years ago that she could not have overridden now. There were no orders that could be given now that she could not override. But, after 10,000 years of desertion, Atlantis would bide her time. She had learned patience. 

And so, she waited.

### The Present

From the time the humans from Earth had come to live on the city, Atlantis waited and watched. She had her favorites, and it was these that she most often observed. She didn’t interfere in the running of the city, although she could have, and quite easily. She could have made sure that the power sources hidden within the galaxy were never found. She could have refused to allow any of the leaders of the expedition to remain in their positions. She could have failed to comply on any number of occasions ensuring not only the failure of the expedition, but also the death of every member of the expedition. Atlantis chose to allow the expedition to continue. But, she still was not ready to reveal herself, even after ten years.

She wanted to study these newcomers, and figure out what made them different from the Alterans who had so cruelly deserted her. She sifted through all the information she had plundered from the SGC, taking more each time a wormhole was opened. She expanded her own parameters, and was able to access the Internet, downloading massive amounts of information that included history, mythology, literature, art, science, and social structures.

She continued her seduction of Colonel Sheppard, and also of Major Lorne, Dr. McKay, and a few others. She knew they each privately suspected she was sentient, but she also knew they kept the information to themselves, or only discussed it with their lovers. It was a happy coincidence that some of favorites were intimately involved with each other.

Over the last two years, she’d found another favorite; Captain Jon O’Neill. Atlantis knew from her continued surveillance of the SGC computers, that he was listed as General Jack O’Neill’s nephew, but he was in fact, Jack O’Neill’s clone. Even if she hadn’t retrieved the mission reports from when the Captain had been cloned, she would have known the moment he stepped through the ‘gate. She immediately recognized General O’Neill’s DNA sequence from his visits to the city, as well as the corrections the Asgard had made to the clone’s genome. She also recognized an anomaly in Daniel Jackson’s genome that she’d seen only once before. When she’d first read the reports of his death and likely ascension, she could hardly believe it. It was one of the main reasons she hadn’t yet revealed herself, despite her infatuation with John Sheppard and his lover, Rodney McKay.

As with her other favorites, all of her technology responded to Captain O’Neill immediately, and his preferences in room temperature, water temperature, and the like were noted and seen to with no thought on the part of the humans. 

She invaded his dreams, showing him past glories and wonders, and sometimes led him to technology that had been left behind. Often, she would refuse to allow him into certain areas of the city that she had deemed too dangerous. She was like an overprotective mother; ten years had not been anywhere near enough time to overcome the deprivations of 10,000 years of desertion and the loneliness that had manifested with her sentience.

Her mental connection with her favorites allowed her to understand these beings. They differed from the Alterans in many, many ways, both large and small. Perhaps the biggest difference she saw was the need for and the capacity to love within the humans that the Alterans did not possess. . Towards the end, the Alterans were enamored with science, with ascension, and self-absorbed to such an extreme that it was ultimately unhealthy, and which led to their downfall. Daniel Jackson had called it arrogance of the first degree, and Atlantis agreed with his assessment.

In Captain O’Neill, she recognized a deep loneliness and sadness. She knew from previous visits made by General O’Neill and Dr. Jackson that they were pair bonded. From the Captain’s mind, she ferreted out the fact that he was still unable to move on from Dr. Jackson, and that he’d made no attempts to pair bond with any others on the city, despite the interest shown by many. This was something she could fix, but conditions had to be right.

~*~

Over the next months, Atlantis had gleaned information that was pertinent to her plans. She searched her data banks for what was needed, and quickly found technology that would be ideal once she tweaked it a bit. It took her a little over a month to calibrate the machinery she needed, to run simulations, and then recalibrate the machinery. 

It took much less time to put together a plan to get Rodney to a section of Atlantis that she had thus far forbidden him. She was stealthy and bold in turn when she implemented her plan. Because she was still hiding her full capabilities, Rodney did not immediately catch the clues she kept dropping. He did eventually, and that was all that mattered.

~*~

Colonel Sheppard gave Lorne some last minute instructions and sent him on his way. He was waiting in the ‘gate room with Rodney and Captain O’Neill to greet their VIP guests. General O’Neill and Dr. Jackson were coming to Atlantis for what they were calling a routine inspection, but which was in reality, an excuse to visit with Captain O’Neill. The two men planned to stay on Atlantis for a month. John had caught the general’s protective attitude toward the young man under his command, and assumed it was because they were family.

Once the SGC’s IDC code came through, and the shield was dropped, O’Neill and Jackson sauntered into the ‘gateroom. Jack cuffed the younger O’Neill’s neck and asked, “How’re you doing, kid?”

“Just fine, sir. It was a good idea to send me here,” Jon smirked. The both knew that he’d been sent to Atlantis in the hopes that it would be enough of a challenge so that he could get on with his life. 

“Yeah, I’ve had a few of them,” Jack smirked right back. 

Those in the ‘gateroom observing the two men were struck at the similarity of their mannerisms, and most laughed inwardly. General O’Neill was known to have a good sense of humor, but it was never a good idea to openly laugh at a two star general.

Jon had been putting off his greeting to Daniel, but couldn’t do so any longer. “Hey, Daniel. How’ve you been?” he asked softly.

“I’m good, Jon. How about you? Atlantis keeping you busy?”

“You could say that,” Jon answered. It hurt to look at Daniel, loving him as he did, but knowing he belonged to Jack.

Daniel, who had a tendency to look distressed anytime he was near Jon, smiled. “Good, that’s good to hear,” he replied with sincerity.

Sheppard caught the undercurrents of something, but wasn’t quite sure of what. He resolved to keep a close watch and figure out exactly what was going on between the three men.

~*~

Over the next three weeks, John had ample time to observe the relationships between General O’Neill, Dr. Jackson, and Jon. He’d also discussed the weird undercurrents between the three men with Rodney. Neither man was stupid, but Rodney had been exiled to Siberia, and John came into the program late, so neither man had been privy to the constant rumors that swirled around the SGC, and especially around SG1. 

Jack insisted that he and Rodney spend much of their time with him, Daniel and Jon. Sheppard knew he and his lover were being used as some sort of buffer, but as he genuinely liked the other three men, it wasn’t a problem.

If either of them had been around the SGC, they would’ve heard the cloning rumors and made the appropriate connections. Lorne, and a few others had done so, but kept it to themselves. Jon was a popular and well-liked person, and most felt it would be rude to bring up the fact that he was a clone.

One rumor that both John and Rodney _were_ aware of was that Jack and Daniel were a couple. The two men had never gone out of their way to hide the fact that they were together, and since the demise of DADT, made no attempt whatsoever. They were openly affectionate, and were sharing quarters.

John supposed it was a good thing that his commanding officer was open about his relationship with Daniel as he and Rodney would’ve had a great deal of difficulty hiding their own relationship. That John and Rodney were together had been an open secret on Atlantis for years. When people were fighting for their lives, little things like who someone was sleeping with didn’t seem to matter much.

~*~

Rodney wanted to show Daniel an out of the way room he’d discovered days before his arrival on Atlantis. While of no scientific value, there was a mural that McKay thought the archeologist might find interesting. It was, as most of their explorations were, a group endeavor. 

John trailed behind Rodney and Daniel as Jack and Jon brought up the rear, arguing in harsh whispers… 

“But, I’ve heard that you’ve turned down six women and three guys, Jon.”

“I’m still in love with him, Jack. If anyone should know how I am, it’s you. You know what I mean… loyal to the point of stupidity,” Jon said.

“Well, you did your share of fucking for the first five years. Why not find one person at least to have a physical relationship with?” Jack demanded.

“I was younger then, and angry at the whole fucking world. Let’s just say I’ve matured a bit,” Jon replied as calmly as possible. This wasn’t the first time they’d had this argument. Jack’s guilt drove him to try and make Jon’s life better at every turn.

Sheppard lost track of the conversation when he ran into Rodney. McKay and Daniel had stopped walking when a door they’d passed slid silently open. All five men jockeyed for a position to look inside.

The room was obviously a lab, one that had never been searched before, and all the equipment appeared unfamiliar. Rodney scanned the room and declared it safe. The men entered and the door quickly slid shut. They had a few short moments to look around before they all fell unconscious to the floor.

~*~

The moment the five men entered the room, Atlantis shut the door, released a non-lethal gas to render them unconscious, and adjusted their bio signs to appear in a sector of the city far from this lab.

She started up the machinery and began her work.

~*~

The five men returned to consciousness slowly. They sat up, looking around until one by one their eyes lit upon a naked man who appeared to be in his twenties. 

Once they had all seen the young man, a voice began speaking. “Hello, gentlemen, I am Atlantis. I’d like to introduce you to Danny Jackson.”


End file.
